Hello Victor, This is OK for use with single-end reads. But, if you have questions about how to exactly interpret the values, the Cufflinks authors would be a good resource, the contact information is in the example of this wiki Support section: http://wiki.g2.bx.psu.edu/Support#Unexpected_scientific_result Hopefully this helps, Best, Jen Galaxy team On 11/3/11 12:44 PM, Li, Jilong (MU-Student) wrote:

Hi,

I want to use cufflinks handle the results of Tophat. Cufflinks uses FPKM to normalize the expression data. I think FPKM is for pair-end reads. right? My reads are single-end. Is it right if I use FPKM?

Thank you very much!

Victor

___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/

-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support